iFull wwPDB X-ray Structure Validation Report ○Oct 4, 2023 – 11:31 PM EDTPDB ID : 6VXS
Title : Crystal Structure of ADP ribose phosphatase of NSP3 from SARS CoV-2Authors : Kim, Y.; Jedrzejczak, R.; Maltseva, N.; Endres, M.; Mesecar, A.; Michalska,K.; Joachimiak, A.; Center for Structural Genomics of Infectious Diseases(CSGID)
Deposited on : 2020-02-24
Resolution : 2.03 Å(reported)
This is a Full wwPDB X-ray Structure Validation Report for a publicly released PDB entry.
We welcome your comments at validation@mail.wwpdb.org
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i symbol.
with specific help available everywhere you see the ○The types of validation reports are described at
http://www.wwpdb.org/validation/2017/FAQs#types.

i were used in the production of this report:
The following versions of software and data (see references ○)MolProbity
Mogul
Xtriage (Phenix)
EDS
Percentile statistics
Ideal geometry (proteins)
Ideal geometry (DNA, RNA)
Validation Pipeline (wwPDB-VP)::::::::

FAILED1.8.5 (274361), CSD as541be (2020)
1.13
FAILED20191225.v01 (using entries in the PDB archive December 25th 2019)Engh & Huber (2001)
Parkinson et al. (1996)
2.35.1

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6VXSi
Overall quality at a glance ○The following experimental techniques were used to determine the structure:
X-RAY DIFFRACTION
The reported resolution of this entry is 2.03 Å.
There are no overall percentile quality scores available for this entry.
MolProbity and EDS failed to run properly - the sequence quality summary graphics cannot beshown.

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6VXSi
Entry composition ○There are 5 unique types of molecules in this entry. The entry contains 2715 atoms, of which 0
are hydrogens and 0 are deuteriums.
In the tables below, the ZeroOcc column contains the number of atoms modelled with zero occupancy, the AltConf column contains the number of residues with at least one atom in alternate
conformation and the Trace column contains the number of residues modelled with at most 2atoms.
• Molecule 1 is a protein called Non-structural protein 3.
Mol

Chain

Residues

1A167

1B

167

Atoms
Total CNO S
1263 803 217 239 4
Total CNO S
1263 803 217 239 4

ZeroOcc

AltConf

Trace

000000

There are 2 discrepancies between the modelled and reference sequences:Chain
A
B

Residue
1
1Modelled
GLY
GLY

Actual-Comment
expression tag
expression tag

Reference
UNP P0DTD1
UNP P0DTD1• Molecule 2 is SULFATE ION (three-letter code: SO4) (formula: O4 S).

Mol

Chain

Residues

2A

1AtomsZeroOcc AltConf
Total O S0054 1Continued on next page...

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Continued from previous page...
Mol Chain Residues
Atoms
Total O S
2A
154 1Total O S
2B
154 1Total O S
2B
154 1

ZeroOcc

AltConf0000006VXS• Molecule 3 is 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID (three-letter code:NHE) (formula: C8 H17 NO3 S).

Mol

ChainResidues

3A

13B

1AtomsTotal C N O
138 1 3Total C N O
138 1 3S1S
1

ZeroOcc

AltConf0000• Molecule 4 is 1,2-ETHANEDIOL (three-letter code: EDO) (formula: C2 H6 O2 ).

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MolChainResidues

4B

1AtomsTotal C O
42 2

ZeroOcc

AltConf00

ZeroOcc

AltConf0000• Molecule 5 is water.
Mol

ChainResidues

5A

69

5B

70

Atoms
Total O
69
69
Total O
7070

MolProbity and EDS failed to run properly - this section is therefore empty.

6VXS

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6VXSiData and refinement statistics ○EDS failed to run properly - this section is therefore incomplete.
Property
Space group
Cell constantsa, b, c, α, β, γResolution (Å)% Data completeness(in resolution range)
RmergeRsym< I/σ(I) > 1
Refinement program
R, Rf reeWilson B-factor (Å2 )Anisotropy
L-test for twinning2
Estimated twinning fraction
Total number of atoms
Average B, all atoms (Å2 )

Value
P1
30.39Å 37.90Å 65.40Å
84.37◦ 82.11◦ 90.11◦
37.71 – 2.03

SourceDepositor

84.8 (37.71-2.03)

Depositor(Not available)(Not available)
3.89 (at 2.03Å)
PHENIX 1.13_2998
0.186 , 0.234
23.10.105< |L| > = 0.47, < L2 > = 0.30
No twinning to report.
2715
24.0

Depositor
Depositor
Xtriage
Depositor
Depositor
Xtriage
Xtriage
Xtriage
Xtriage
wwPDB-VP
wwPDB-VP

Depositor
Depositor

Xtriage’s analysis on translational NCS is as follows: The largest off-origin peak in the Patterson
function is 9.62% of the height of the origin peak. No significant pseudotranslation is detected.

Intensities estimated from amplitudes.
Theoretical values of < |L| >, < L2 > for acentric reflections are 0.5, 0.333 respectively for untwinned datasets,
and 0.375, 0.2 for perfectly twinned datasets.
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6VXS

iModel quality ○iStandard geometry ○MolProbity failed to run properly - this section is therefore empty.

4.2

i
Too-close contacts ○MolProbity failed to run properly - this section is therefore empty.

4.3

i
Torsion angles ○

4.3.1

i
Protein backbone ○MolProbity failed to run properly - this section is therefore empty.
4.3.2

iProtein sidechains ○MolProbity failed to run properly - this section is therefore empty.
4.3.3

i
RNA ○

MolProbity failed to run properly - this section is therefore empty.

4.4i
Non-standard residues in protein, DNA, RNA chains ○There are no non-standard protein/DNA/RNA residues in this entry.

4.5i
Carbohydrates ○There are no monosaccharides in this entry.

4.6

i
Ligand geometry ○7 ligands are modelled in this entry.
In the following table, the Counts columns list the number of bonds (or angles) for which Mogul
statistics could be retrieved, the number of bonds (or angles) that are observed in the model andthe number of bonds (or angles) that are defined in the Chemical Component Dictionary. The
Link column lists molecule types, if any, to which the group is linked. The Z score for a bond

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6VXS

length (or angle) is the number of standard deviations the observed value is removed from theexpected value. A bond length (or angle) with |Z| > 2 is considered an outlier worth inspection.
RMSZ is the root-mean-square of all Z scores of the bond lengths (or angles).

-Bond lengths
Counts RMSZ #|Z| > 2
13,13,130.66
1 (7%)

Bond angles
Counts RMSZ #|Z| > 2
16,17,17
0.58
0-13,13,13
4,4,4
3,3,3
4,4,4
4,4,4
4,4,4

16,17,17
6,6,6
2,2,26,6,6
6,6,6
6,6,6

Mol

Type

ChainResLink

3NHE

B

203

32
42
2
2

NHE
SO4EDO
SO4SO4SO4A
AB
B
B
A

202
201
202
201
204
203

0.66
0.13
0.44
0.14
0.140.151 (7%)
00000

0.67
0.06
0.44
0.07
0.08
0.08

000000In the following table, the Chirals column lists the number of chiral outliers, the number of chiral
centers analysed, the number of these observed in the model and the number defined in theChemical Component Dictionary. Similar counts are reported in the Torsion and Rings columns.
’-’ means no outliers of that kind were identified.
Mol
3
34

Type
NHE
NHE
EDO

ChainB
A
B

Res
203
202
202

Link-Chirals-Torsions
0/7/15/15
0/7/15/15
1/1/1/1

Rings
0/1/1/1
0/1/1/1-All (2) bond length outliers are listed below:
Mol
33Chain
BARes
203
202

TypeNHENHE

Atoms
O3-S
O3-S

Z
2.18
2.17

There are no bond angle outliers.
There are no chirality outliers.
All (1) torsion outliers are listed below:
Mol
4

Chain
B

Res
202

TypeEDO

Atoms
O1-C1-C2-O2

There are no ring outliers.
No monomer is involved in short contacts.

Observed(Å)
1.55
1.55

Ideal(Å)
1.47
1.47

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Other polymers ○There are no such residues in this entry.

4.8i
Polymer linkage issues ○There are no chain breaks in this entry.

6VXS

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Fit of model and data ○iProtein, DNA and RNA chains ○EDS failed to run properly - this section is therefore empty.

5.2i
Non-standard residues in protein, DNA, RNA chains ○EDS failed to run properly - this section is therefore empty.

5.3i
Carbohydrates ○EDS failed to run properly - this section is therefore empty.

5.4i
Ligands ○EDS failed to run properly - this section is therefore empty.

5.5i
Other polymers ○EDS failed to run properly - this section is therefore empty.

6VXS